Yes the updates worked! I was actually about to comment on the github issue you posted about the similar issue with applywarp when you added the comment about flirt. -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A&M Institute for Neuroscience Texas A&M University College Station, TX
On Wed, Jun 5, 2019 at 2:02 PM Harms, Michael <[email protected]> wrote: > > > Try the very latest master, which should resolve this issue. (I was just > working on this 30 min ago). Please let us know if it works. > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: [email protected] > > > > *From: *<[email protected]> on behalf of Joseph Orr < > [email protected]> > *Date: *Wednesday, June 5, 2019 at 1:52 PM > *To: *Simon Wein <[email protected]> > *Cc: *HCP Users <[email protected]>, Wilhelm Malloni < > [email protected]> > *Subject: *Re: [HCP-Users] Error while running > "GenericfMRIVolumeProcessingPipeline.sh" > > > > We ran into the same problem with *flirt*. In FSL 6.0.1, *flirt *can't > take a 4D file as a reference, but it could in fsl v5. Adding a line before > 289 to extract the first volume of PhaseTwo_gdc, and modifying flirt > accordingly fixes the problem: > > > > ${FSLDIR}/bin/fslroi ${WD}/PhaseTwo_gdc ${WD}/PhaseTwo_gdc_slice -1 -1 -1 > -1 -1 -1 0 1 > > ${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref > ${WD}/PhaseTwo_gdc_slice -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out > ${WD}/SBRef2PhaseTwo_gdc > > -- > > Joseph M. Orr, Ph.D. > > Assistant Professor > > Department of Psychological and Brain Sciences > > Texas A&M Institute for Neuroscience > > Texas A&M University > > College Station, TX > > > > > > On Sat, May 25, 2019 at 8:48 AM Simon Wein < > [email protected]> wrote: > > Thank you very much for your support. > > In our pipeline we have set *$GradientDistortionCoeffs = "NONE",* so line > 189 in > > > > https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh > <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_HCPpipelines_blob_master_global_scripts_TopupPreprocessingAll.sh&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=THI4wxtmV_mHRAFlqo6fSROIYYps7PUMkLs13L56dHs&s=8WyIfhjNJpj6y0N1VFd0l72m8q5_3JN4yAteiQWVgIM&e=> > > > > was unfortunately skipped. But we could avoid the error by modifying line > 196 to: > > > > fslmaths ${WD}/BothPhases.nii.gz -mul 0 -add 1 ${WD}/Mask > > > > > > Mask.nii.gz then has properties: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *filename Mask.nii.gz size of header 348 data_type FLOAT32 > dim0 4 dim1 104 dim2 104 dim3 72 dim4 6 > dim5 1 dim6 1 dim7 1 vox_units mm time_units s > datatype 16 nbyper 4 bitpix 32 pixdim0 1.000000 > pixdim1 2.000000 pixdim2 2.000000 pixdim3 2.000000 > pixdim4 7.700000 pixdim5 0.000000 pixdim6 0.000000 > pixdim7 0.000000 vox_offset 352 cal_max 0.000000 > cal_min 0.000000 scl_slope 1.000000 scl_inter 0.000000 > phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown > slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 > toffset 0.000000 intent Unknown intent_code 0 > intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 > 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 -1.995593 > 0.092717 0.094922 93.702583 qto_xyz:2 -0.105543 -1.976261 -0.288537 > 118.937881 qto_xyz:3 0.080419 -0.292910 1.976799 -43.901993 qto_xyz:4 > 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left > qform_yorient Anterior-to-Posterior qform_zorient > Inferior-to-Superior sform_name Scanner Anat sform_code 1 > sto_xyz:1 -1.995594 0.092714 0.094922 93.702583 sto_xyz:2 -0.105540 > -1.976261 -0.288537 118.937881 sto_xyz:3 0.080420 -0.292910 1.976799 > -43.901993 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 > sform_xorient Right-to-Left sform_yorient Anterior-to-Posterior > sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 > descrip 6.0.1 aux_file * > > The previously mentioned problem with FSL 6.0+ fslmaths could be avoided. > > Would you consider this as a good workaround, or would you recommend > something else? > > > > But in a later stage, we got another error: > > > > > > > *Image Exception : #75 :: 3D only method called by higher-dimensional > volume. 3D only method called by higher-dimensional volume. Could not open > matrix file > /loctmp/CUDA/DATA/VP_101/rfMRI_REST1_PA/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef2PhaseTwo_gdc.mat > Cannot read input-matrix* > > > > The file *"SBRef2PhaseTwo_gdc.mat*" was not created, so the problem might > be in line 289 in *"TopupPreprocessingAll.sh":* > > > *${FSLDIR}**/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref > ${WD}/PhaseTwo_gdc -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out > ${WD}/SBRef2PhaseTwo_gdc* > > > > Properties of *SBRef.nii.gz* are: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *filename SBRef.nii.gz size of header 348 data_type UINT16 > dim0 3 dim1 104 dim2 104 dim3 72 dim4 1 > dim5 0 dim6 0 dim7 0 vox_units mm time_units s > datatype 512 nbyper 2 bitpix 16 pixdim0 1.000000 > pixdim1 2.000000 pixdim2 2.000000 pixdim3 2.000000 > pixdim4 0.730000 pixdim5 0.000000 pixdim6 0.000000 > pixdim7 0.000000 vox_offset 352 cal_max 0.000000 > cal_min 0.000000 scl_slope 1.000000 scl_inter 0.000000 > phase_dim 2 freq_dim 1 slice_dim 3 slice_name > sequential_increasing slice_code 1 slice_start 0 slice_end 0 > slice_duration 0.000000 toffset 0.000000 intent Unknown > intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 > intent_p3 0.000000 qform_name Scanner Anat qform_code 1 > qto_xyz:1 -1.995593 0.092717 0.094922 93.702583 qto_xyz:2 -0.105543 > -1.976261 -0.288537 118.937881 qto_xyz:3 0.080419 -0.292910 1.976799 > -43.901993 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Right-to-Left qform_yorient Anterior-to-Posterior > qform_zorient Inferior-to-Superior sform_name Scanner Anat > sform_code 1 sto_xyz:1 -1.995594 0.092714 0.094922 93.702583 > sto_xyz:2 -0.105540 -1.976261 -0.288537 118.937881 sto_xyz:3 0.080420 > -0.292910 1.976799 -43.901993 sto_xyz:4 0.000000 0.000000 0.000000 > 1.000000 sform_xorient Right-to-Left sform_yorient > Anterior-to-Posterior sform_zorient Inferior-to-Superior file_type > NIFTI-1+ file_code 1 descrip TE=31;Time=163300.630;phase=0 > aux_file Single-band_reference* > > > > > > And properties of *PhaseTwo_gdc.nii.gz:* > > > > *filename PhaseTwo_gdc.nii.gz* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > * size of header 348 data_type UINT16 dim0 4 dim1 104 > dim2 104 dim3 72 dim4 3 dim5 0 dim6 0 > dim7 0 vox_units mm time_units s datatype 512 nbyper > 2 bitpix 16 pixdim0 1.000000 pixdim1 2.000000 > pixdim2 2.000000 pixdim3 2.000000 pixdim4 7.700000 > pixdim5 0.000000 pixdim6 0.000000 pixdim7 0.000000 > vox_offset 352 cal_max 0.000000 cal_min 0.000000 > scl_slope 1.000000 scl_inter 0.000000 phase_dim 2 freq_dim 1 > slice_dim 3 slice_name alternating_increasing_2 slice_code 5 > slice_start 0 slice_end 0 slice_duration 0.000000 toffset > 0.000000 intent Unknown intent_code 0 intent_name intent_p1 > 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner > Anat qform_code 1 qto_xyz:1 -1.995593 0.092717 0.094922 93.702583 > qto_xyz:2 -0.105543 -1.976261 -0.288537 118.937881 qto_xyz:3 0.080419 > -0.292910 1.976799 -43.901993 qto_xyz:4 0.000000 0.000000 0.000000 > 1.000000 qform_xorient Right-to-Left qform_yorient > Anterior-to-Posterior qform_zorient Inferior-to-Superior sform_name > Scanner Anat sform_code 1 sto_xyz:1 -1.995594 0.092714 0.094922 > 93.702583 sto_xyz:2 -0.105540 -1.976261 -0.288537 118.937881 > sto_xyz:3 0.080420 -0.292910 1.976799 -43.901993 sto_xyz:4 0.000000 > 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient > Anterior-to-Posterior sform_zorient Inferior-to-Superior file_type > NIFTI-1+ file_code 1 descrip TE=58;Time=162508.120;phase=0 > aux_file * > > Employing *flirt* from FSL 5.0.6 worked again, but we were not sure, how > to modify line 289 properly for FSL 6.0.1. > > Thank you for your time. > > > > Simon > > > > > > > > > > >>> "Glasser, Matthew" <[email protected]> 05/22/19 9:09 PM >>> > > There could be a bug here related to new FSL 6.0+ fslmaths behavior. > Please try modifying: > > > > > https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh > <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_HCPpipelines_blob_master_global_scripts_TopupPreprocessingAll.sh&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=THI4wxtmV_mHRAFlqo6fSROIYYps7PUMkLs13L56dHs&s=8WyIfhjNJpj6y0N1VFd0l72m8q5_3JN4yAteiQWVgIM&e=> > > > > line 189 to: > > > > ${FSLDIR}/bin/fslmaths ${WD}/PhaseOne_mask_gdc -mas > ${WD}/PhaseTwo_mask_gdc -ero -bin -Tmin ${WD}/Mask > > > > Matt. > > > > *From: *<[email protected]> on behalf of Simon Wein < > [email protected]> > *Date: *Wednesday, May 22, 2019 at 8:28 AM > *To: *Timothy Coalson <[email protected]> > *Cc: *Wilhelm Malloni <[email protected]>, " > [email protected]" <[email protected]> > *Subject: *Re: [HCP-Users] Error while running > "GenericfMRIVolumeProcessingPipeline.sh" > > > > Thank you very much for your suggestion. > > We already use FSL 6.0*.1 *(and Freesurfer 6.0.0), sorry for my > inaccuracy. > > The output of "fslhd ${WD}/BothPhases" is: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *filename BothPhases.nii.gz size of header 348 data_type INT32 > dim0 4 dim1 104 dim2 104 dim3 72 dim4 6 > dim5 1 dim6 1 dim7 1 vox_units mm time_units s > datatype 8 nbyper 4 bitpix 32 pixdim0 1.000000 > pixdim1 2.000000 pixdim2 2.000000 pixdim3 2.000000 > pixdim4 7.700000 pixdim5 0.000000 pixdim6 0.000000 > pixdim7 0.000000 vox_offset 352 cal_max 0.000000 cal_min > 0.000000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 > freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 > slice_start 0 slice_end 0 slice_duration 0.000000 toffset > 0.000000 intent Unknown intent_code 0 intent_name > intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 > qform_name Scanner Anat qform_code 1 qto_xyz:1 -1.995593 0.092717 > 0.094922 93.702583 qto_xyz:2 -0.105543 -1.976261 -0.288537 118.937881 > qto_xyz:3 0.080419 -0.292910 1.976799 -43.901993 qto_xyz:4 0.000000 > 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient > Anterior-to-Posterior qform_zorient Inferior-to-Superior sform_name > Scanner Anat sform_code 1 sto_xyz:1 -1.995594 0.092714 0.094922 > 93.702583 sto_xyz:2 -0.105540 -1.976261 -0.288537 118.937881 sto_xyz:3 > 0.080420 -0.292910 1.976799 -43.901993 sto_xyz:4 0.000000 0.000000 > 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient > Anterior-to-Posterior sform_zorient Inferior-to-Superior file_type > NIFTI-1+ file_code 1 descrip 6.0.1 aux_file * > > > > > > The output of "fslhd ${WD}/Mask.nii.gz" is: > > > > *filename Mask.nii.gz* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > * size of header 348 data_type FLOAT32 dim0 4 dim1 104 > dim2 104 dim3 72 dim4 3 dim5 1 dim6 1 > dim7 1 vox_units mm time_units s datatype 16 nbyper > 4 bitpix 32 pixdim0 1.000000 pixdim1 2.000000 > pixdim2 2.000000 pixdim3 2.000000 pixdim4 7.700000 > pixdim5 0.000000 pixdim6 0.000000 pixdim7 0.000000 > vox_offset 352 cal_max 0.000000 cal_min 0.000000 > scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 > slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 > slice_end 0 slice_duration 0.000000 toffset 0.000000 intent > Unknown intent_code 0 intent_name intent_p1 0.000000 > intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat > qform_code 1 qto_xyz:1 -1.995593 0.092717 0.094922 93.702583 > qto_xyz:2 -0.105543 -1.976261 -0.288537 118.937881 qto_xyz:3 0.080419 > -0.292910 1.976799 -43.901993 qto_xyz:4 0.000000 0.000000 0.000000 > 1.000000 qform_xorient Right-to-Left qform_yorient > Anterior-to-Posterior qform_zorient Inferior-to-Superior sform_name > Scanner Anat sform_code 1 sto_xyz:1 -1.995594 0.092714 0.094922 > 93.702583 sto_xyz:2 -0.105540 -1.976261 -0.288537 118.937881 > sto_xyz:3 0.080420 -0.292910 1.976799 -43.901993 sto_xyz:4 0.000000 > 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient > Anterior-to-Posterior sform_zorient Inferior-to-Superior file_type > NIFTI-1+ file_code 1 descrip 6.0.1 aux_file * > > > > We noticed that running "*${FSLDIR}/bin/fslmaths ${WD}/BothPhases -abs > -add 1 -mas ${WD}/Mask -dilM -dilM -dilM -dilM -dilM ${WD}/BothPhases_fsl5" > *seems to work with FSL 5.0.6 at least. The header of the image > *"BothPhases_fsl5 > "*, generated with FSL 5.0.6 , is: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *filename BothPhases_fsl5.nii.gz sizeof_hdr 348 data_type > FLOAT32 dim0 4 dim1 104 dim2 104 > dim3 72 dim4 6 dim5 1 dim6 1 > dim7 1 vox_units mm time_units s datatype 16 > nbyper 4 bitpix 32 pixdim0 0.000000 pixdim1 > 2.000000 pixdim2 2.000000 pixdim3 2.000000 pixdim4 > 7.700000 pixdim5 0.000000 pixdim6 0.000000 pixdim7 > 0.000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 > scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 > freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 > slice_start 0 slice_end 0 slice_duration 0.000000 time_offset > 0.000000 intent Unknown intent_code 0 intent_name > intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 > qform_name Scanner Anat qform_code 1 qto_xyz:1 -1.995593 > 0.092717 0.094922 93.702583 qto_xyz:2 -0.105543 -1.976261 > -0.288537 118.937881 qto_xyz:3 0.080419 -0.292910 1.976799 > -43.901993 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Right-to-Left qform_yorient Anterior-to-Posterior > qform_zorient Inferior-to-Superior sform_name Scanner Anat > sform_code 1 sto_xyz:1 -1.995594 0.092714 0.094922 93.702583 > sto_xyz:2 -0.105540 -1.976261 -0.288537 118.937881 sto_xyz:3 > 0.080420 -0.292910 1.976799 -43.901993 sto_xyz:4 0.000000 > 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient > Anterior-to-Posterior sform_zorient Inferior-to-Superior file_type > NIFTI-1+ file_code 1 descrip FSL5.0 aux_file * > > > > > > All the best > > > > Simon > > > > > > >>> Timothy Coalson <[email protected]> 05/21/19 8:57 PM >>> > > This may not be related to your particular problem, but you need to have > FSL 6.0.1 for some of the pipelines (MR FIX in particular). Using fslhd on > the BothPhases and Mask files should give others on the list some > information to work with. > > > > Tim > > > > > > On Tue, May 21, 2019 at 8:18 AM Simon Wein < > [email protected]> wrote: > > Dear all, > > > > we are experiencing problems when performing the fMRI volumetric > processing with "GenericfMRIVolumeProcessingPipeline.sh": > > > > Image Exception : #3 :: Attempted to multiply images of different sizes > terminate called after throwing an instance of 'std::runtime_error' > what(): Attempted to multiply images of different sizes > /loctmp/CUDA/Pipelines-master_fs6/global/scripts/TopupPreprocessingAll.sh: > line 269: 10710 Aborted ${FSLDIR}/bin/fslmaths > ${WD}/BothPhases -abs -add 1 -mas ${WD}/Mask -dilM -dilM -dilM -dilM -dilM > ${WD}/BothPhases > > > > > > Environment: > > 1. Debian 9.0 > > 2. HCP pipeline 4.0.0 > > 3. Workbench 1.3.2 > > 4. FreeSurfer 6.0 > > 5. FSL 6.0 > > 6. gradunwarp (HCP) 1.0.3 > > > > > > We would be thankful for any help! > > > > Kind regards > > Simon > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=THI4wxtmV_mHRAFlqo6fSROIYYps7PUMkLs13L56dHs&s=Co6qIFMSawWKWXPRkI8-12oQS5Y5aMnkmG57bC0NW-4&e=> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=2DacYG1sMdSK4b-tDh8Rdaef9gjfxdD4A9MriM4ArPs&s=yc9abkhaxT9RYmxJkjaQmLLcI80b5LXwcIX7ztZqiR0&e=> > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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